Mycobiology.  2022 Aug;50(4):231-237. 10.1080/12298093.2022.2116816.

Re-Identification on Korean Penicillium Sequences in GenBank Collected by Software GenMine

• Seo CW
• Kim SH
• Lim YW
• Park MS

• KMID: 2538250
• DOI: http://doi.org/10.1080/12298093.2022.2116816

Abstract

Penicillium species have been actively studied in various fields, and many new and unrecorded species continue to be reported in Korea. Moreover, unidentified and misidentified Korean Penicillium species still exist in GenBank. Therefore, it is necessary to revise the Korean Penicillium inventory based on accurate identification. We collected Korean Penicillium nucleotide sequence records from GenBank using the newly developed software, GenMine, and re-identified Korean Penicillium based on the maximum likelihood trees. A total of 1681 Korean Penicillium GenBank nucleotide sequence records were collected from GenBank. In these records, 1208 strains with four major genes (Internal Transcribed Spacer rDNA region, b-tubulin, Calmodulin and RNA polymerase II) were selected for Penicillium reidentification. Among 1208 strains, 927 were identified, 82 were identified as other genera, the rest remained undetermined due to low phylogenetic resolution. Identified strains consisted of 206 Penicillium species, including 156 recorded species and 50 new species candidates. However, 37 species recorded in the national list of species in Korea were not found in GenBank. Further studies on the presence or absence of these species are required through literature investigation, additional sampling, and sequencing. Our study can be the basis for updating the Korean Penicillium inventory.

Keyword

GenBank; inventory; Penicillium; re-identification; tree-based identification